Rigging and bone orientation
There was some good input from Nathan Vegdahl on this exact subject in the bf-animsys mailing list last year. This is all subjective, of course, but it makes it easiest for animators if the axes throughout your rig are consistent first and foremost. This is a copy/paste from his email(s) to the list: 


  The main rules-of-thumb that I try to follow are:
  - The x-axis should be the "primary" axis of rotation for any given control.
  - Rotation in the "primary" direction on the x-axis should result in a
  positive rotation angle (meaning that if it were euler, the x component of
  the rotation would be positive).
  - For bones that are free-floating and/or don't have any particular
  relationship to other controls (the root control is a good example), align
  all of their axes with the world axes.
  
  In the first two rules, "primary" is often subjective or ambiguous,
  depending on the control, so you just have to use your best judgement and
  experiment what it feels like to use it as an animator.
  
  It's important also to note the reason for doing any of this at all.  In
  all 3d animation software, keeping bones aligned well helps keep the rig
  better organized for the rigger.  It's also important for animators when
  e.g. working in the f-curved editor.  But in Blender it's particularly
  important for animators, because one of the major interaction models for
  tranforms is via hotkeys, using the x, y, and z keys to specify axes.





  Oh, I should also say: the choice of x vs z axis as the "primary" rotation
  axis is arbitrary.  I choose x because it's the first letter in "xyz".  But
  z is just as good.  What matters is consistency within the rig (or within
  the project if it's a larger project).


I generally follow Nathan's conventions when I rig in blender, although the same principles follow in any software I use. Again, this is all subjective, so your mileage may vary and you might find a better convention for your particular rig. It is also important to take into account your rotation orders on your controls. XYZ might be better suited for a primary axis of Z+ in your rig, whereas an order of YZX might be better suited with X+ as primary axis. 

bf-animsys January 2014